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UCSC Genome Browser (University of California Santa Cruz Genome Browser)
The UCSC genome browser is a publicly available database of a large number of vertebrate and invertebrate genomes created by the University of California, Santa Cruz. It is built on a MySQL database and is useful for analyzing your genome of interest and multiple genome comparisons. The genome browser was initially established in 2000 by Jim Kent, a graduate student at the time at The University of California, Santa Cruz. It was first utilized the view the work in progress in the Human Genome Project. http://en.wikipedia.org/wiki/UCSC_Genome_Browser#History How to Search and Use the UCSC Genome Browser When you first open the Genome Browser Gateway, a number of categories are present to search the genome of interest. Group gives the option of choosing mammal, invertebrate, etc. The genome indicates which genome within that group you are interested in. For example, under mammal you can pick the human genome. Assembly allows you to choose which reference genome you are interested in using. The newest assembly of the human genome was created in 2009 and is called Feb. 2009 (GRCh37/hg19) created by the Genome Reference Consortium. From here you can search for a gene or a region of the genome using the position, gene symbol or search terms. The website details the types of search terms which can be used. Once your gene or region of the genome is found, there are several annotation tracks that are displayed by default and some which can be added to the customization of the user. Some examples of these are tracks are potential single nucleotide polymorphisms, nucleotide conservation and locations of repeats. The gene structure is also shown as thick boxes, thin boxes and lines which correspond to coding regions, untranslated regions and introns respectively. Direction of the gene, whether it is in the sense or antisense position, is displayed with an arrow. The user also has the ability to zoom in and out of the gene. Zooming in will show the actual nucleotide sequence. Clicking on a gene or mRNA transcript gives you more information, such as genetic association studies linked to that gene, mRNA secondary structure and orthologous genes in other species. 1,2 An Example of Utilization of the UCSC Genome Browser in Research The UCSC Genome Browser can be used for a number of research projects as has been indicated by the references section on the genome browser website. Genome wide methylation sequences were generated by Fei Gu., et al. in an article published in 2013 which utilized 191 patient samples and 41 breast cancer cell lines to create a cancer-specific methylated DNA library for human breast cancer and endometrial cancer. From this study the authors created a means of searching the epigenetic characteristics of both breast cancer and endometrial cancer. The authors created methylated DNA libraries of both cancer types using MBD-Cap Sequencing technology. Once the sequences were aligned to the human genome, they created a database for searching the data based on a number of tracks. Some of these tracks, such as the H3K4me1 histone modification and CpG island track were both taken from the UCSC genome browser. In this study, the browser was used to create a more specific means of searching two cancer methylomes. The browser could be used in many different types of studies from genomics, to single gene studies or even protein interaction studies. 3 References 1. UCSC Genome Bioinformatics. http://genome.ucsc.edu/ 2. Guide to the UCSC Genome Browser. Learn Science at Scitable. http://www.nature.com/scitable/ebooks/guide-to-the-ucsc-genome-browser-16569863/contents 3. Gu, F. et. al. CMS: a web-based system for visualization and analysis of genome wide methylation data of human cancers. PloS One. 2013 April 22.; 8 (4). http://www.ncbi.nlm.nih.gov/pubmed/23630576